rs11048230

chr12-25772238-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.163 in 152,070 control chromosomes in the GnomAD database, including 2,903 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.16 (2903 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.862

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24672 AN: 151952 Hom.: 2898 Cov.: 31

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.0979

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.0210

Gnomad SAS AF: 0.0512

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.0950

Gnomad OTH AF: 0.154

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.163 AC: 24714 AN: 152070 Hom.: 2903 Cov.: 31 AF XY: 0.161 AC XY: 11970 AN XY: 74354

Gnomad4 AFR AF: 0.335

Gnomad4 AMR AF: 0.0976

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.0210

Gnomad4 SAS AF: 0.0516

Gnomad4 FIN AF: 0.130

Gnomad4 NFE AF: 0.0950

Gnomad4 OTH AF: 0.153

Alfa AF: 0.135 Hom.: 330

Bravo AF: 0.168

Asia WGS AF: 0.0450 AC: 155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	10
Dann	Benign	0.63

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11048230; hg19: chr12-25925172;